Kathleen Kish July 29, 2022
Source files to model extracellular stimulation of a retinal ganglion cell. Associated with the following paper: Kathleen Kish, Scott Lempka, and James Weiland. "Modelling extracellular stimulation of retinal ganglion cells: theoretical and practical aspects." doi: https://doi.org/10.1088/1741-2552/acbf79
Included is the Python code (jupyter notebook) to generate a morphologically-realistic mammalian retinal ganglion cell, as well as .mod files for biophysical modeling in the NEURON software environment.
The file "RGC_Model.ipynb" is the base script that generates the neuron model, and allows for
- Intracellular Current Injection
- Extracellular Stimulation from an Ideal Point Source
- Extracellular Stimulation from a Disc Electrode (where extracellular voltage is imported from a .txt file)
The files "Axon_Ellipse.ipynb" and "Extracellular_Stimulation.ipynb" contain functions called by the base script that generate the axon trajectory and apply an extracellular stimulus pulse, respectively.
The files "capump.mod", "mammalian_spike.mod", and "xtra.mod" contain the biophysical equations used by the NEURON simulation environment (https://neuron.yale.edu/neuron/). These .mod files must be compiled prior to using the model.
The files "interpxyz.hoc", "setpointers.hoc", and "RGC_morph_4.hoc" contain functions called by the base script that relate to the 3-D morphology of the cell.
The file "Voltages_from_COMSOL.txt" contains the extracellular voltage at the center of each neural compartment, and was generated by our finite element model of an epiretinal disc electrode near the retinal surface. The file "COMSOL Model Reduced.mph" contains the geometry of our finite element model (the mesh and solution were deleted to reduce the file size).